Axonal distribution within the retinal nerve fiber layer (RNFL) measured by optical coherence tomography (OCT) correlates with axonal viability and integrity. To investigate correlations between RNFL and MRI measures of axonal loss in MS patients. Fifty one remitting-relapsing MS patients, 20 with a history of optic neuritis (MS-ON), 31 without optic neuritis (MS N-ON), and 12 healthy control subjects (HC) were included in the study. RNFL was measured by OCT and brain atrophy was assessed by MRI. The average RNFL in the affected eye (AE) in the MS-ON group was significantly lower than the RNFL in the MS N-ON (p = 0.01) and in HC (p = 0.01). The average RNFL in the unaffected eye (UE) and RNFL in MS N-ON were also lower than HC, but this value did not achieve significance. In MS N-ON a lower average RNFL was associated with an increased T1 lesion volume (p = 0.03) and T2-lesion volume (p = 0.001). The RNFL in MS N-ON was also associated with a reduction of BPF and %gm fraction (p = 0.01, p = 0.02 respectively). In MS-ON there was a much weaker, non-significant correlation between RNFL thickness and T1, T2 volume, BPF, %gm and %wm fractions that might have resulted from a pronounced post-inflammatory local optic nerve atrophy in AE. The RNFL measured by OCT may be useful as a surrogate marker for assessment of brain atrophy in MS.